top of page
mmu_ciGart_1740
Basic information of circular RNA
PanCircBase ID:
mmu_ciGart_1740
mm39_Chr. Position ID:
chr16|91436359|91438099|-
Gene name:
Gart
Transcript:
ENSMUST00000023684.14
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
1740
Exon/intron sizes in nt:
1740
Flanking exon/introns:
chr16:91436339-91438099
Splice length:
1740
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGGGCAAAAAGTCACCTTTAAAGGGCAGGTGTTTTATAAAGTCACTTTAGTGGTTAAAAAAAAAAAAAAAAAAAAGTTGCCAGGCAGCCCTTGGGAGGCAGAGGCAAGTGAATCTCTTGAGTTTGAGGCCACAGAGTGAGTTTCAGGACAGCCAGGGCTACACAGAAAAACCATGTCTTTAAAAAAAAAAAAAACGGGGCTAGAGAGATGGCTAAGCAGTTAAGAGCACCAACTGTTCTCCCAGGGGTCCTGAGTTCATTTCCCAGCAACTACGTGGTAGCTCACAACCATCTGTAATGGGATCTGATGCCCTCTTCCGGTGTGTCTGAAGACAGCTACAGTGTACTCAAATACAATAAATAAATAAATGTTTTAAAAAAAAAGAAGAAGAAGCCGGGCAAGTGGTGGCACACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCCGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAATTCCAGGACAGCTAGGGCTATACAGAGAAACCCTGTCTCAGAAAAAAAAAGAAAAAAGAAAGAAAAACAAAAAGTAAAAAATGTTTACTTCTTAGGCTTTCACAGGTTTATATTGAATTAATTATGGAAATATACTCTCAATAAAATAACTCATTTCCTTTATACCACTAAAATAAGATCGGATTCTCCAGTATTTGGGAGGTAGAAGCTAAAGGGTCAGTTCAAAGCCAGCCTGGACTACGTGGATCCAAAAGGAGAAGGAATTAAAAAAGAAACACTCTGTGTGTGCTTCTCTTGAATAATCTTGTCGACTGTATGTTGATGTCTTCACTATTGAGAAATCTCTAAGAGGAAGCACAGCAAGGCTAATGGCAATCCTCCTGCTTCAGCCTCCTTAGTGCTAGGATAGTAGGCGTAACCCGCCATACCCAGCAGAGTTTCTGAATTTGTAAGCTTTTTTTTTCAACAACTTATTTACTCTGTGTGTGTGTGCACGTGCAAGTGTGCGTGTACACATGGGCACACGACTCTACACTTGTATCAGACTATAGCTTGTAAGAGTCAAGTTCTCTCCTTCTACCACGTGGGTTCCAGGAATGAACTCAGGTCAGCCACCTCGCTGACCCTAGATCTTTCTTTATTCATTCTTCATCCTGCAAGGCTCCTTTTTTTCCAGGGGTAGTGGGCAAGAGAGGATTAAATGTGTAGTCCAGGCTGTCACTCTGTAGACCATGCTGGCCTCAAACTCAAGAGATTCACCTGCCTCTGCCTCTGCCTCTGCCTCCCAAGTGCTAAGGTTAAAGATGTGTGCTCCCACTGCCCAGCTCCTACACTGACTGTTGTTACCCATAGCCATGCGCCTTGGGTAAGTGACAGCTTAGTTACTTACTTTGGCTAAGCCTCCTTCCAGATCTCCAGCCCACAACATTGCTTTGTGTGTTCTAGAAATGGTCTGTGGGTGTCTGCCAGTGTTAGTCTCCTACAGCAGTATCCCTTACGTAAGTGAGAGGCTTTGCTTTGTATTTTAAAGATTATCTGTTCTACAGGTCTGCTTATTTTTTATATGATTCTTCCTTATGTGACCTAACTATATGTGGAAAAAGCAAAATTGTGCATGCTTTATGATCAAAATTACAAAGGAATTTTTAAAAATTTTTGGCAAGTAGTACCTGAAACAATGCTGGAATCATCTTTTTCTGTGTCCCTTTCAATTTTGCTAAACCATTCTGTTAAAAAGCACAGACCACTAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGAAACAATGCTGGAATCA
58.5
GGCTGCCTGGCAACTTTTT
59.55
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTACCTGAAACAATGCTGGA
57.21
GGCTGCCTGGCAACTTTTT
59.55
176
PCR template sequence:
AATTTTTGGCAAGTAGTACCTGAAACAATGCTGGAATCATCTTTTTCTGTGTCCCTTTCAATTTTGCTAAACCATTCTGTTAAAAAGCACAGACCACTAAGTGGGCAAAAAGTCACCTTTAAAGGGCAGGTGTTTTATAAAGTCACTTTAGTGGTTAAAAAAAAAAAAAAAAAAAAGTTGCCAGGCAGCCCTTGGGAGGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
20
Interacting miRNAs (#binding sites)
mmu-miR-709(2), mmu-miR-3470b(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-103-3p(1), mmu-miR-30e-5p(1), mmu-miR-200c-3p(1), mmu-miR-146a-5p(1), mmu-miR-30a-5p(1), mmu-miR-30c-5p(1), mmu-miR-298-5p(1), mmu-miR-203-3p(1), mmu-miR-381-3p(1), mmu-miR-30b-5p(1), mmu-miR-218-5p(1), mmu-miR-340-5p(1), mmu-miR-107-3p(1), mmu-miR-705(1), mmu-miR-3087-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACAGACCACTAAGTGGGCAAAAAGT
siRNA sets
ACTTTTTGCCCACTTAGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIGART_1740_ORF_1
0.7379
-0.230253165
0.052059538
276
ORF sequence:
ATGCTTTATGATCAAAATTACAAAGGAATTTTTAAAAATTTTTGGCAAGTAGTACCTGAAACAATGCTGGAATCATCTTTTTCTGTGTCCCTTTCAATTTTGCTAAACCATTCTGTTAAAAAGCACAGACCACTAAGTGGGCAAAAAGTCACCTTTAAAGGGCAGGTGTTTTATAAAGTCACTTTAGTGGTTAAAAAAAAAAAAAAAAAAAAGTTGCCAGGCAGCCCTTGGGAGGCAGAGGCAAGTGAATCTCTTGAGTTTGAGGCCACAGAGTGA
Peptide sequence:
MLYDQNYKGIFKNFWQVVPETMLESSFSVSLSILLNHSVKKHRPLSGQKVTFKGQVFYKVTLVVKKKKKKKLPGSPWEAEASESLEFEATE
IRESfinder result
IRESfinder score
0.800227957
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page